The Omniformer: Ultimate Shinobi
by Jonathan579
Summary: After sacrificing himself to defeat Malware. The Omniformer finds himself in a world of ninjas. Can he learn to survive in this new world? More importantly, will he ever return home?
1. Chapter 1

Jonathan Bolanos. Better known as the Omniformer, is the wielder of the awe inspiring device known as the Omnitrix who has just turned nineteen a few months ago. Many things have changed for our hero in the last three years, like taking a leave of absence from earth's mightiest heroes, the Avengers after defeating Galactus the Devourer of Worlds. He was ready to start being a solo hero when the Plumbers assigned Jonathan a new partner named Rook who just graduated from Plumber's Academy. 

At first Jonathan was annoyed that he was getting a new partner but after a few missions, he and Rook became very good friends. During the this time-frame, Jonathan unlocked new aliens and mastered the Evolutionary Function allowing a few of his aliens to evolve into new powerful transformations called the Ultimate Forms.

Now dealing with the paparazzi, fighting villains old and new, dealing with likes of J. Jonah Jameson, and stopping criminals both alien and metahuman. Jonathan had his work cut out for him. It safe to say that he was more mature and serious, always being a hero because it was the right thing to do, and being more strategic when it comes to facing stronger foes.

So now onto the events of the last couple of months, well he was fighting for his life. There was a new villain named Khyber the Huntsman who wanted to make Jonathan into one his trophies. There was also an evil Cerebrocrustacean named Dr. Psychobos who created a knock-off version of the original Omnitrix that contained the natural predators of most of Jonathan's aliens. Not to forget hid old enemy Malware, a psychotic Galvanic Mechamorph who was obsessed with gaining the powers of the Omnitrix. With these three joining forces, it was a tough situation for our hero. 

The Nemetrix was a device that contained non sentient predators of the Omnitrix aliens, so only a non-sentient being could wield it. That's why Khyber gave it to his dog Zed. Every battle proved to be very difficult as Khyber knew how to counter every alien Jonathan turned into by having Zed transform into that alien's predator. Our hero was not alone though. He received help from Rook and the Amazing Spider-Man and his team. They proved to very valuable allies in a lot of critical situations. 

Despite Khyber having the advantage, Jonathan and Rook always forced him to retreat. The Ultimate Forms really came in handy as Zed stood no chance against their overwhelming power.

The battle soon reached its breaking point as the Faction invaded Galvan Prime to kill Azmuth. But they didn't count on Azmuth teleporting our heroes to the planet. After a long battle Jonathan was able to defeat Zed by using a whistle to make the dog obey him and subdue Psychobos. But Unfortunately Khyber was able to escape. But the true threat appeared as Malware became more powerful by absorbing the helix destroying Galvan B in the process and used its pieces to infect Galvan Prime. 

Azmuth tried to reason with by telling him there was still time for him to stop so they could work together to make him complete. However, the planet's defenses attacked Malware which caused him to believe that Azmuth was trying to destroy him instead of curing him. It was then that the final showdown between the Omniformer and Malware began as Jonathan constantly rotated his aliens to fight this monster. The battle soon reached its climax when Jonathan as Way Big stomped on Malware.

"Is it over?" said Way Big. 

"Nah, dude it's never that easy" said Spider-Man as he latched himself onto Way Big's shoulder. 

"You're right; it would take a lot more than that to beat Malware. You go and search for everyone else while I finish things here" said Way Big as Spider-Man quickly followed Jonathan's order and jumped off his shoulder. 

"Come on Malware, I know you're still alive" Way Big growled as black and red goo started to form around his foot.

"No not this time" Way Big yelled as he got the goo off his leg without much effort. 

"You are a fool Jonathan Bolanos" said Malware as he now stood about Way Big's height. 

"Yeah, well it takes one to know one" said Way Big as he punched Malware and then kicked him backwards he then crosses his arms together as he fires his cosmic ray at Malware, obliterating the top half of his body.

"There, that should do it" said Way Big as he began walking toward Malware's remains but little did he know that it was far from over. 

"ARGGH…what!" yelled Way Big as he was being engulfed by Malware's parts. His eyes widened in horror as he saw Malware assuming another form, this one resembling a large dinosaur. It was immense, easily dwarfing Way Big.

"Do you see how your loyalty to Azmuth is repaid" Malware laughed as Way Big was being consumed by the black liquid. "Only despair and utter destruction await you!" 

"NO, I won't let you win!" screamed Way Big as he slammed the Omnitrix dial and in flash of green light, Way Big suddenly grew in size, with blue joining his red skin, along with two white horns that joined his large crest.

"**ULTIMATE WAY BIG!"**

"You think that is going to turn the tides!" yelled Malware.

Ultimate Way Big crouched, then jumped very high into the air and then came back down with a well-aimed kicked straight onto Malware's head which sent him flying. The impact creating a crater fifty feet deep.

Ultimate Way Big didn't let as he shot many energy disks at Malware causing him great pain. But it was not enough as Malware quickly regenerated. Malware did the unthinkable as he grabbed Ultimate Way Big and absorbed him into his body. 

"Goodbye Jonathan Bolanos" barked Malware.

_**Inside Malware**_

"Uuhh…where am I?" Jonathan groaned as he found himself inside a red and black space. His eyes widened as he realized he was actually inside Malware!

"Damn, I'm totally helpless now!" growled Jonathan as he found out he couldn't move any part of his body.

"This is bad, this is really really bad" said Jonathan in despair. He was supposed to be the hero, but he went ahead and got himself into this. He had to do something but the question was how?

He soon came up with a solution; he just hoped his parents would forgive him for it "The Omnitrix…it has a self-destruct system. If I allowed it to charge for only three minutes it will cause an explosion so devastating that it would not only wipe out Malware but will kill me as well" said Jonathan as a tear rolled down his cheek.

"Mom, Dad, David, IDON, Rook, Azmuth, Peter, Logan …Ester. I will miss you all and I'm sorry that I had to die like this. I hope I done you all proud" Jonathan closed his eyes and smiled. 

"I hope this command still works in this new Omnitrix. Omnitrix, self-destruct in 230 seconds."

_**Destruct sequence completed and engaged. Detonation in t-minus 230 seconds.**_

"230" 

"229"

…

… 

… 

…

"3" 

"2" 

"Say goodbye Malware" Jonathan chuckled 

"1" 

"BOOOOMMMM" 

With a deafening explosion Malware was annihilated leaving no trace left of him at all. Azmuth's eyes turned watery as the realization hit him. Jonathan Bolanos was dead.

"Jonathan…he used the self-destruct mode. He sacrificed himself to save all of us" Azmuth spoke with a shaken voice.

Everyone couldn't believe that Jonathan was dead and they wept silently as they mourned the young hero.

Was it true? Was the Omniformer really dead? That is simply not the case; this story is far from over…in fact it has only just begun.

**Hello everyone, this is UltraJohn567 coming at you with another story. If you want to know more about my OC Jonathan Bolanos, visit my deviantart page as it will have a detailed summary on the Omniformer Saga. Let me know what you think of this story in the comments section as you can expect the next chapter to come out soon.**


	2. Chapter 2

The only thing Jonathan felt was pain. Deep agonizing pain. The next thing he knew was that a flash of green light engulfed him. Jonathan felt his every part of his body being ripped away. He wanted to scream but he couldn't. He wondered if this was what death felt like. 

Time once again came to a stop as another wave of green light engulfed Jonathan and this time he completely blacked out from what occurred. There was nothing but utter darkness. For a moment Jonathan felt like was going through a narrow tube.

Next thing he knew he was falling from 2000 feet straight to the ground. Jonathan then realized that he was not dead but was going to be if he didn't stop himself from falling. Despite the increasing momentum Jonathan managed to activate the Omnitrix and transform.

In a flash of green light Cannonbolt appeared it his place then tapped the dial again to transform into Ultimate Cannonbolt. Curling into a ball, dashing toward the ground with increased momentum.

The spiked silver ball smashed onto the surface with a loud crash. With a green flash Jonathan reverted to his human form on one knee panting very heavily. 

Luckily for Jonathan, thanks to Ultimate Cannonbolt's immense durability he wasn't very injured just very exhausted. Jonathan soon fell on his back still breathing hard. After two hours Jonathan gained enough strength to stand back up.

He took a look at his surroundings, seeing that he was in the middle of a large forest with a small river nearby. 

"How did I end up all the way from Galvan Prime to some forest?" wondered Jonathan as he went to the river to clean his face and drink some water. After washing his face clean he looked at the water's surface and caught his reflection. 

"What the, I'm fifteen again?!" yelled Jonathan as he looked like he did when he was fifteen. 

Why was he four years younger? Was this a side effect from the explosion? He had so many questions but no one was around to answer them. He hoped that Professor Paradox and Azmuth would find him soon. 

He checked the Omnitrix to make sure his all of his aliens were there and sure enough they were. Even the Ultimate Forms were still available which was a bonus.

"I guess I have to go and see if there's a town nearby" said Jonathan as he began walking down a dirt path. After fifteen minutes he came across a small town with buildings reminiscent of ones from Japan. After entering the city he saw something that made him stop in his tracks. Some men were dragging a woman and a kid out of their home. A crowd was nearby but no came to their rescue. 

"Let us go you bastards!" the kid shouted. 

"Now that's a rude thing to say, look like I'm going to have to teach you some manners kid" A man smirked. 

"Please let my son go. Take me but let him go please" The woman pleaded with tears in her eyes.

"That's why we're here Tsunami. Don't worry Gato will take care of you. A pretty lady like you now belongs to him" Another man laughed maniacally as he put Tsunami's chi up.

"I suggest you step away from that woman before things get very ugly" a voice yelled. Everybody turned around and saw a fifteen year old boy standing there. By the looks of it, it was clear that he was a foreigner.

"What was that brat?" the man said as he glared at Jonathan.

"You heard me, step away from her or I'm going to beat you within an inch of your life scumbag" Jonathan yelled and walked forward.

"Heh, or what?" the man laughed.

"I warned you" Jonathan grinned as he activated the Omnitrix and turned into a red four-armed creature.

"FOURARMS!"

The two men were shocked as Fourarms dashed forward and punched the man who was holding Tsunami knocking him out.

"Are you alright mam?" asked Fourarms extended his hand to help Tsunami. 

"You shouldn't have done that freak, now you die!" with a yell 3 of the thugs who were armed with weapons charged at Fourarms. Fourarms evaded their blows without much effort and started hitting them with his massive fists.

"5 seconds, a new record" Fourarms smirked as he turned back to normal.

"Thank you so much" Tsunami bowed. 

"Just doing the right thing Mam" Jonathan smiled.

"Stop trying to act like a hero. You've just delayed things. Now Gato will send more men and he will kill us. If you want to survive then run away" the kid yelled.

"Hey, I just saved your life back there kid!" Jonathan scowled. 

"Listen young man, you may be brave and strong for your age and that you can turn into that red creature. But you need to get out of here before more of those men come. You have no idea who Gato is don't you?" said an old man named Tazuna.

"I don't care who this Gato person is, you can't just let him terrorize you people for the rest of your lives and I'm going to do whatever it takes to take him down!" shouted Jonathan with a determined look on his face.

Then Jonathan heard the sound of clapping, He turned and saw a samurai was clapping with an arrogant smirk on his face.

"Can I help you?" said Jonathan with a raised eyebrow

"Commander Fuzo, that kid beat us all up" said one of Jonathan's victims who were barely conscious.

"This kid beat you all up? He doesn't look like much" laughed Fuzo.

"You won't be laughing once I'm through with you" snarled Jonathan. 

"What are you gonna do about it?" said Fuzo.

In a flash of green light Jonathan transformed into a browned skinned dinosaur that stood over 30 feet tall.

"HUMUNGOUSAUR!"

To say Fuzo was surprised was an understatement "What the hell are you?!"

Humungousaur grinned "I'm the one who's going to kick your ass into next week" He then clapped his hands, which created a powerful shockwave that sent Fuzo flying into a nearby building. 

Humungousaur tapped the Omnitrix dial and turned back into Jonathan, he walked up to a dazed Fuzo.

"Give this message to your boss; if I ever see him or any of his goons I'm going to go pay him a little visit, which won't be as pleasant as it sounds.

"You did you beat Gato's men. You really are a hero" said Inari as he hugged Jonathan. 

"It was no big deal."

"Is there any way we can thank you? I didn't even get your name. 

"My name is Jonathan Bolanos, but I'm also known as the Omniformer."

Everyone cheered as they called out Jonathan's name declaring him a true hero. 

Another chapter finished! Thank you for all the kind reviews. I didn't think this story would get that much attention in one day and I'm glad for that. Next chapter Jonathan will meet Team 7 during the fight with Zabuza. By the way I appreciate if you guys can give me some ideas for future chapters. 


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